SEQUENCHER CONTIG ASSEMBLY IMVERTED SOFTWARE

The most popular genetic marker for mycological research questions at and below the genus level is the nuclear ribosomal internal transcribed spacer (ITS) region, a ca.

SEQUENCHER CONTIG ASSEMBLY IMVERTED SOFTWARE

The highly automated nature of many sequence analysis pipelines similarly makes software suites susceptible to several kinds of sequence errors - such as incorrect taxonomic annotations - since these automata are often built to accept certain classes of information at face value.

While very experienced users may perhaps be able to look through such broken data, many others may not be in a position to do so, particularly not since a growing number of people from outside mycology - even outside the academia - now use fungal sequence data as a part of their work. On the contrary, there are indications that the proportion of several classes of compromised sequences - such as chimeras and reverse complementary sequences - increases over time ( Abarenkov et al. 2008), but none have succeeded in halting the continual submission of substandard entries to the databases. Several studies have reported on the various shortcomings of the public DNA sequence corpus (e.g., Gilks et al. When such entries are made publicly available through the international sequence databases, their compromised integrity becomes a problem not only for the researcher who generated them in the first place but for the entire mycological - indeed, scientific - community. Sequences of compromised technical quality or of incorrect taxonomic or ecological annotations are major contributors in this respect in that they may lead researchers to erroneous results and conclusions. 2007).įor all their advantages, molecular data do not solve all open research questions in mycology, and examples of where the misuse and misinterpretation of molecular data hampered mycological progress are easy to point out ( Nilsson et al. 2009), and the landmarks include the establishment of a phylogenetic backbone and a classification system for the fungal kingdom ( Blackwell et al. Today, DNA sequences represent a key source of information in nearly all branches of mycology, including systematics, taxonomy, and ecology ( Stajich et al. For these and other reasons, mycologists were quick to embrace molecular (DNA sequence) data as a research tool in the early 1990s ( Horton and Bruns 2001 Anderson and Cairney 2004). Furthermore, discriminatory yet easily assessed morphological characters are something of a rare commodity in mycology, and morphology alone often falls short of providing unequivocal species identification and delimitation. As a result, most sampling sites and habitats host a much greater fungal diversity than the above-ground view offered by fruiting bodies would lead the observer to believe ( Porter et al. Many fungal lineages do not seem to produce tangible fruiting bodies, and for those that do, the factors promoting - and acting against - fruiting body formation are only partly understood.

The inconspicuous and largely subterranean or endophytic nature of much of fungal life presents a challenge to mycology.

Sequencher contig assembly imverted